BtaINT0041668 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012849 | COL4A1
Description
Bos taurus collagen, type IV, alpha 1 (COL4A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001166511]
Coordinates
chr12:88898050-88898422:-
Coord C1 exon
chr12:88898255-88898422
Coord A exon
chr12:88898140-88898254
Coord C2 exon
chr12:88898050-88898139
Length
115 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATCCTTCTGTCCGGCCACAGGTC
3' ss Score
9.96
Exon sequences
Seq C1 exon
GCCCCCCCGGAGTGAAAGGAGAGAAAGGCTTCCCTGGCTTCCCAGGCCTGGACATGCCAGGCCCCAAAGGAGACAAAGGGTCCCAGGGGCTCCCCGGCCTGACGGGGCAGTCTGGGCTGCCTGGCCTTCCTGGACAGCAGGGCACCCCCGGCCAGCCTGGCATTCCAG
Seq A exon
GTGAGCGACTGTGAGCCCCACCCACGTGGGCCTGGGGAGGTGCCTCCCGGCTCTTGTTCACGACTCTCGTTCGGCCTCCGCCACCAACATTCACGATCCTTCTGTCCGGCCACAG
Seq C2 exon
GTCCCAAGGGAGAGATGGGAGTCATGGGGACTCCAGGGCAGCCCGGCTCGCCAGGGCCAGCGGGCGTGCCAGGATTGCCAGGTGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012849:ENSBTAT00000035335:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(30.0=31.6),PF0139113=Collagen=PU(66.1=71.9)
A:
NA
C2:
PF0139113=Collagen=PD(32.3=64.5),PF0139113=Collagen=PU(40.0=77.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCGGAGTGAAAGGAGAGAA
R:
TGCCCTGGAGTCCCCATG
Band lengths:
204-319
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development